Welcome Mainak Deb! Mainak will work on the Upgrading DevoLearn project (#3.1).
If you would like to learn more about Open-source and Open Science, take a look at this directory for more information.
This project revolves mainly around devolearn, a PyPI package that aims to make deep-learning models more accessible for research in developmental biology.
What can I do before GSoC?
You can start out by reading about the C. elegans embryo, and then move on to either help us in improving our current models or add new ones. You can also help us solve some of the Github issues (if any) on the corresponding project boards. Please keep the mentors updated with your progress!
Experience or mastery of PyTorch, Numpy/Pandas, and OpenCV/Imageio/FFMPEG tools are desired. Proficiency in writing scalable and modular code would be helpful.
EPIC Dataset image data
Processed C. elegans Developmental Data DevoWorm Github
You will be improving upon the Digital Bacillaria project link, which was started in the Summer of 2019. This year our main aim is to enhance the existing deep learning model. For the sake of uniformity, you might have to move the model from Tensorflow to PyTorch at first. You will be involved in pre-processing and analyzing microscopy videos from our database of Bacillaria phenotype and movement.
What can I do before GSoC?
You can ask one of the mentors to direct you to the data source and you can start working on it. Please feel free to raise questions/discussions regarding your approach to the problem. Check out some of our community references for a better ideas of how your project might fit into the organization.
DevoWormAI: link
Digital Bacillaria project: link
Raw video (microscopy) data link
Here are the tab-delimited versions of the data link
Paper with analysis from 2019 link
Recent presentation on Bacillaria movement link
PyTorch/Tensorflow (PyTorch will be preferred because all our other models are on that framework already) Wrangling with video data Building a simple GUI on top of the model to run it on local systems (on Linux/windows/macOS) General knowledge about Diatoms
This project will build upon the specialized microscopy techniques to develop a shell composed of projected microscopy images, arranged to represent the full external surface of a sphere. This will allow us to create an atlas of the embryo’s outer surface, which in some species (e.g. Axolotl) enables us to have a novel perspective on neural development. You will build a computational tool to visualize these 4D data.